John's City
by HyperMint
Summary: Title may change. The Crew throws a party, but John goes missing...Rodney remembers something. McShep Friendship nonslash sorry
1. Chapter 1

I was watching "Rising Parts One and Two" again and I noticed something. I don't know if anyone else noticed, but I thought it was very interesting.

Disclaimer: I don't own Stargate: Atlantis but it would have been nice if I could.

Chapter one

John Sheppard was not a happy camper right at this moment.

It did not matter that it was storming outside and it did not matter that he had been grounded for some strange and unknown reason, because it didn't really matter at all.

Never mind that his birthday was coming up, either.

No. The one thing that irked him more than that was being ignored.

Yes, Ronon was on the Mainland and Teyla was on loan to another team and John was alright with that. Really. After all, the two wouldn't be gone that long.

It just seemed that no matter what he did or how he did it, no one cared. It even seemed that people were avoiding him.

He really didn't understand it.

John was actually beginning to think that he had done something wrong, but he just didn't know what, yet.

Doctors Carson Beckett and Elizabeth Weir always seemed to be busy and was always getting called away from him in the middle of a conversation. Even Major Lorne wasn't hanging out with John like he used to and it was honestly ticking him off.

It kinda didn't bother him that Dr. Radek Zelenka and Dr. Rodney McKay were almost living in the labs nowadays. It just bothered him that they didn't ask him to come down to turn something on or something else to that effect.

So, it was on a stormy afternoon that Colonel Sheppard decided to get some dessert in the mess hall purely out of boredom. All paperwork was done and processing, no getting dragged down to the labs by the scruff of his neck, no meetings, no training the new recruits because they were on the Mainland with Ronon and Lorne getting drilled to within an inch of their lives…

John sat down at an empty table with a mug of coffee and a tray laden down with the desserts that he adored. As he sipped his coffee, he remembered something from a long time ago.

"_I promise that you won't amount to anything in life. Even your friends will show their true colors. Sure, go into the Force if you like, but nothing will ever come of it. You will just be an annoying little bug that people only put up with because they have to."_

John shook his head. 'You're wrong,' he thought. 'I am something here. My friends and co-workers don't think like that. I'm sure of it. Right, Atlantis?'

He felt a bit silly asking the city, but just about choked on his pudding when he felt a sort of warmth envelope him like a blanket.

He looked around, startled, as he finished his tray. "There is just no way that could've been… Ah, but I've dealt with stranger things in my day. I think. Oh, well. Maybe Rodney could use some help down in the lab."

He looked around again and told himself that he would ask Rodney about something like this being possible.

Rodney McKay was busy with calculations on his laptop when he heard the door open. Without turning, he said, "I told you before to stop bothering me while I'm working. You have work to do so stop coming down to my lab trying to heckle me when I could be trying to prevent an explosion from wiping us out of existence. Go bother someone else for a change, I'm busy and I don't have time to waste on idiots like you. And if you don't like it, well, I don't care. I have more important things to waste my precious time on and not on people who don't do-"

Rodney stopped his tirade and turned when he heard the door close.

"Huh," he shook his head.

"_Weir to Rodney,"_ came the voice over his earpiece.

"What's up?"

"_Am I interrupting something?"_

"No, I just finished talking, well, ranting at that annoying scientist that's been bugging me for the last two hours. Can't seem to get the message that I don't want him down in my territory."

"_You treat all of them like that, Rodney."_

"Yeah, but this one in particular…"

"_I get it. I was just checking on how the preparations are coming along."_

"Wonderfully, Elizabeth. Teyla is going to be back a day early, and the other two are just finishing up on the Mainland. We have it all set. You?"

"_It hasn't been easy, but I'm pretty sure that John has no idea about our plans."_

"He had better not. I didn't agree to this whole surprise party for Sheppard, only to find that he figured it out."

"_Don't worry. Everyone has taken precautionary measures and we know that he has no inkling whatsoever."_

"Hope you're right. I've never really thrown a party for anyone before. Jeez, what if he doesn't like the party? Or the present I'm gonna give him? I never really thought-"

"_Rodney! He'll like it. Both of them. And it's because it is from his friends and he will be especially happy that his best friend got him something."_

"If you're sure… Well, alright, then, I suppose. I just can't help but feel that something is about to go horribly wrong…"

"_Don't worry. I'm sure it's just nerves. Well, I have to check in with the others. Weir out."_

Rodney went back to work, still unable to shake that foreboding feeling…

Review! First Atlantis fic…


	2. Chapter 2

John's City

There is a bit of a mention of the episode _Grace under Pressure_

Chapter Two

John finally slowed down, breathing hard from his unscheduled run, when he reckoned he was as far from the others as he could be without being on the Mainland. Lucky for him, there were still parts of the city that hadn't been explored yet. Unluckily, though, John knew that the city's version of the LSD could pick him up no matter where he was.

He looked around at the room he found himself in. Needless to say, he was very surprised to find himself in, what looked like, a storage room. There were shelves filled with countless things, pieces, and general other things that would have Rodney, Radek Zelenka, and the others salivating with excitement. The room was roughly half the size of the mess hall and maybe one times the size of it. There were shelves running the length of three walls and more between.

John, tired, walked over to the only wall that didn't have shelves and sat in front of it. Having decided to stop thinking, he instead studied the wall, wondering why there were no shelves. It didn't really make all that much sense.

'But then,' he thought to himself, 'nothing makes that much sense ever since I stepped foot on this city.'

He turned and scooted so that he could lean back against the wall and remembered his first trip through the 'Gate. After reminiscing for half an hour, something triggered in his mind. He sat up and looked straight ahead as he thought out loud.

"When I first stepped through the Stargate," he began to the room, which had closed and locked without him knowing, "I looked around and Rodney was with me. We had paused in front of the stairs, which lit up. As we continued, lights started coming on by themselves. Now, knowing what I do now, which is more than I did then, and knowing that lights come on in the presence of the ATA gene and that Rodney didn't have the gene then, there is only one possible way that those lights could have come on by themselves: I woke the city up."

He paused. "I really should go tell Elizabeth and Rodney." Then remembering the cold shoulder he had been getting, he shook his head. "No. I should wait til I've calmed down. Then after explaining to them, I'll go to the gym and take out the rest of my anger on that punching bag." He stood and leaned against the wall. "I can't believe it. I woke this city up. That goes to show you," he told the memory from the mess hall. "I am good for something. I don't care what you say."

Rodney, though, was a different story. After hearing what he said in the labs, John was very hesitant to talk to him again. 'I guess he was right. My friend did show his true colors. To top it all off, I thought this birthday was going to be different. I guess not.'

Cocking an ear, John shivered as he heard a clap of thunder echo throughout the city. It certainly reminded him of his other birthdays. One of them being the day of that storm that the Genii decided to take over.

"Well, I don't know. I guess tomorrow will be only us two, eh, Atlantis?"

John nodded. He leaned back and found himself leaning past where the wall should have been. He tried to grab something, but it was too late.

John lost his balance, hit the floor hard, and slid a few feet down a ramp into three inch deep water.

AAAAAAA

Rodney finally dragged himself out of the lab and into the mess hall where the lead party planners were congregated around two tables pushed together.

Ronon and Teyla had managed to sneak into Atlantis without drawing too much attention and was currently having Major Lorne explain to them about why they had to isolate John.

"See, the Colonel has this way about him that just lets people talk to him. You know, enough to spill minor secrets, like a surprise birthday party that needs to stay secret from him…"

Rodney settled next to Elizabeth and stretched his arms. "Everything going according to plan?"

"Imagine my surprise when I find out that everything is going the way we want it to for a change. Now, I'm waiting for the Wraith to show up or something like that," Elizabeth said, referring to the many times that their plans had ended up being shot to hell.

"Oh, I can imagine, alright," Rodney watched as Dr. Carson Beckett wandered over to the bar for a mug of hot cocoa and some biscuits. "I'm slightly surprised, myself."

Rodney searched the crowd, finding the absence of one John Sheppard. "Shouldn't the Colonel be here, too?"

Elizabeth followed his search and said, "It _is_ unusual for him to miss out on dinner… Perhaps he's already been here?"

"Maybe."

As the hour grew late, the crowd dwindled until only SGA-1, sans John, and Elizabeth remained.

"Dr. Weir," Teyla approached her. "When should we be ready for John's arrival in the mess hall?"

"Around lunchtime, barring any emergency. In any case, we should make sure that he doesn't chance upon the decorating committee before it's time," Elizabeth decided. "I think it's time for bed."

"Of course," Teyla nodded and lead Ronon out, leaving Rodney and Elizabeth alone to finish their drinks.

"So," Rodney drained his coffee, "I wonder how likely it is that Sheppard won't kill us for springing this on him."

"He'll be mad, alright, but I won't go that far. I could be wrong, though," she mused. "We all know how John hates surprises… I should be getting to bed, myself. Try not to stay up all night, Rodney," Elizabeth admonished as she strode past on her way out.

"Wouldn't dream of it," Rodney called after her, getting a raised eyebrow in return. As she disappeared from sight, he leaned back in his chair thinking. Granted, he was teased constantly by John for thinking too much, but he felt a reason for this.

Getting up, he disposed of his cup and left to roam the halls, thinking of all the times he had walked them before. Stopping near a particular window, he remembered a time not too long ago that he had noticed something about his friend.

FLASHBACK

"_So, I said, 'I know how to file, but that didn't mean I was good at it.' Boy, the look on her face was priceless," John said to a bunch of others, military and civilian alike, who laughed._

_Rodney had turned the corner just in time to see the group scatter for their allotted posts. John spotted him and said, "McKay! Got a minute?"_

"_Oh, sure, Colonel, like I'm ignoring my job right now," he said sarcastically, but John just grabbed his arm and steered him next to a window, nonetheless._

"_I was hoping to talk to you. Beckett needs to be picked up from the Mainland and I was volunteered for the job. I was hoping you could go with me?" John casually asked, but his eyes looked to be pleading._

_Rodney shook his head. "As much as I'd love to go on a joyride in a Jumper, I actually have work to do. Why don't you ask Conan or Xena to go? I'm sure they'd love the chance to take a break."_

"_Teyla's already on the Mainland and Ronon's off-world with Major Lorne training the new batch that just came in. I just thought you could… Never mind. I'll get ready to go."_

_With that, John turned and headed to his quarters to get organized, but not before Rodney saw the lonely look in his eyes. Or the defeated slump of his shoulders._

_An hour later, Rodney showed up in the Jumper Bay all geared up and complaining about the idiots who were probably going to blow half of Atlantis sky high before they came back. John had pleasantly lit up at the unexpected arrival and went about loading the Jumper with more of a bounce. At Elizabeth's look, Rodney quietly said, "I thought he could use the company of someone who called Earth home and who thought of him as anything but a waste of time. Besides, he asked me to go. Couldn't very well say 'no' to my best friend, could I?" 'Not with that look that I had felt myself wear many a time in my schooling,' he added silently._

"_Of course not," Elizabeth nodded, before Jumper One was all ready to go. She saw them off and headed back to her office._

FLASHBACK END

Rodney knew that he had changed his mind when John walked off as though his friend said that they didn't want to be friends anymore. He couldn't have that. To top it off, he rarely had a true friend that he trusted not to do something that could hurt him. John was his friend and sometimes it was like reading an open book with him.

John was desperate for a friendly face that he could trust and trade friendly, if not feather-ruffling, insults with.

A sudden clap of thunder snapped the brooding Rodney out of his thoughts. 'Strange, I thought the storm had stopped,' he thought looking out. 'Oh, well. Time for bed anyway.'

TTTTTTT

"Ow," John said as he came out of his sleep. "Wonder how long I've been out for." He sat up, finally noticing the 3 ½ in. water that surrounded him. "I guess the question is: where did I end up after the wall disappeared?"

Standing up, John swayed slightly as he tried to check out the situation. He leaned against the ramp, for want of a better word, and looked around. It was the size of the Meeting Room, if not bigger, and had a table in the center. The surface was filled with little pieces of metal and other things that could have been something when assembled together. Along the walls were what looked like the Ancients version of boxes. After sitting on one, John decided that it was indeed what they were. Looking at his watch, he saw that it was just past three in the morning and that he was sort of hungry. He cursed as he remembered that he had detoured to his quarters just before taking off to parts unknown to get rid of the radio. He didn't want to be disturbed and that was the best way to do it.

Now he wished he hadn't. Thinking back, he supposed that, even though he didn't hit the floor that hard, the few hours of sleep he had accumulated over the past two weeks had finally caught up with him.

John shook his head. "I need to get out of here. I can't really expect everyone to just drop whatever they're doing and get me out of mess after mess. This once, I think it best if I get myself out of this. Now, how would I go about doing said getting out?"

John stood up and picked up the box he was sitting on. To his surprise, it was light, but sturdy enough to hold his weight. Putting it up against the ramp, he stood on it only to see that he had another half foot or so before he could reach the wall, which had decided to solidify again.

Shaking his head, he got to work stacking more boxes.

LLLLLL

Rodney woke up, groggy as usual. Looking at his clock, he saw that it was almost 8:00 in the morning and that John hadn't woken him up before.

Scrubbing his face tiredly, Rodney pulled himself out of bed to get ready for the new day.

Finished dressing, he snagged the blue covered present from his secret hiding place and headed to the Infirmary to stash it. Carson had said that John wasn't about to visit the place willingly and that it was safe until they could relocate the bunch to the cafeteria where the decorating group was doing their job.

Fingering the flat object, Rodney couldn't hold back a small smile at the thought of what lay inside.

After having secured a safe spot for the fragile present, he headed to the lab, when the lights started to flicker.

Racing the rest of the way, he yelled for the others to check the power and other things.

AAAAA

"Anything?" Elizabeth wanted to know about the flickering lights.

"No, not a thing. Everything's normal," Rodney sat heavily in her office, stumped. They had run diagnostics until they ran out of ideas.

That had been two hours ago. Apparently, the running theory was, the raging storm outside, which had stayed the night, had something to do with it. What, they weren't sure, but it was only a matter of time.

"We'll keep working on it, but I don't think it's that important anymore at this point."

"Alright, then. Keep me updated. On a lighter note, John hasn't been seen hanging around the mess hall, so that's proof that he hasn't caught on yet. Hopefully, we can keep this up for another two hours," Elizabeth mused.

"Sure thing. I'll go around to his quarters in a few minutes and drag him off to keep him busy in the labs. That way he'll be too busy to suspect anything."

"Good."

After more chatting, Rodney left the Control Tower like he had many times in the past and went downstairs. At the base, however, he paused to study it, a memory flitting by. He just couldn't grab onto it at the moment and decided that it wasn't important. If it decided it was, then it would flit past again.

Shaking his head, he headed off to the labs, then swung by John's quarters. The door was closed and Rodney knocked.

"Colonel? Open up. I have some things that I need you to 'turn on', as you put it." Getting no answer, he tried again. "John, please come down to the lab with me. I need your help." Again, no answer.

"I'm coming in," he warned before doing just that. He stepped in his friend's quarters and looked around for said friend. "Well, he's not here. Maybe he went to the gym," Rodney mumbled as he took a good look around. He turned to leave when his eye caught on a picture of himself and the person he was looking for.

It had been taken in the Jumper Bay shortly after he was released from Carson's care after his stint in that sinking Jumper. John was sitting up against the side of one of the Jumpers and right next to Rodney. They had taken a break and were eating a packed lunch that John had thoughtfully brought along. Or maybe it was because that when Rodney was hungry, he complained about the smallest things.

In either case, they were digging in and John had struck up a conversation, about which Rodney could vaguely recall. Whoever had snapped the picture did so when Rodney had begun to gesture with his hands to illustrate what he was talking about. John was pouring some beverage out of the thermos into a cup, listening with half an ear.

Rodney remembered falling silent soon after and glanced at his lunch companion. Suffice it to say, he thought that the other had fallen asleep, so it was with surprise that he saw John leaning against the Jumper, staring off into space with a true, happy smile on his face. That intrigued him, even now. Usually, Rodney saw a happy smile only when faced with a potentially life threatening adventure, sometimes known as a trip through the Stargate. This smile, though, was as relaxed as Rodney had ever seen it. He briefly wondered if any of the others saw the smile.

Rodney shook his head, snapping out of his fond memories. He had a job to do and he wasn't going to give up so easily.

'Alright, Colonel,' he thought stepping into the hallway, 'I am going to find you and we are going down to my lab. I think that will be enough to keep you busy.'

NNNNN

AN: Sorry about the wait. A 7 page chapter should make up for it.

8-10-07


	3. Chapter 3

-1AN: sorry. I'm working on an 'Utena' one-shot right now to get rid of the writer's block for Harry Potter and the new Defense Teacher or Defense Teacher, as I'm calling it.

Now, before I get on with the story, I would like to thank my reviewers from the first two chapters:

For chapter one: anon. dajaje and anon. elfyelfyelfy, Stealth Dragon, jasminesmommy, and Stargate Groupie.

For chapter two: anon. ladybird21, Stealth Dragon, Stargate Groupie, darkangel24700, and to my tenth reviewer, may2002, as well as cat4444 and Ditzyleo

Thank you and keep'em coming.

Mention of The Defiant One

Also, there may be some language in here…

Chapter 3

John stretched as he stood, surveying his work.

The boxes were stacked much like the steps on a pyramid. The base consisted of three boxes and had three more stacked on top of them. The 'stairs' coincided with the shape of the 'ramp' and reached the wall. Surprisingly, there were enough boxes in the room to do it and, to John's disbelief, there was still more left. In fact, if John didn't know any better, he would've sworn that there were more boxes now than when he had first started with.

'Of course, that is a possibility,' he thought. 'This is, after all, Atlantis. You never really know in this place.'

John climbed his 'stair case' to the top. The end was exactly where the floor should have been had it continued through the door. John put his hands on the surface and pushed as hard as he could.

Needless to say, the wall didn't move.

After ten minutes of yelling, hitting, and glaring at the wall, John gave up. There was no way out. John even yelled nonsense words but to no avail.

'Wait a minute. How'd I get in here anyway?' John thought a minute. 'The wall didn't give way until I said, it look like it's just you and me, Atlantis. Or something like that. Maybe if I say that it'll open. Like Aladdin.'

John tried it. Once again, it didn't work. He ran his fingers through his hair, messing it up even more.

"I guess there really is nothing I can do. I guess I just have to wait for someone." Now, he regretted leaving his radio, but it seemed like a good idea at the time.

He sighed and climbed back down. "I guess I wait. What a day," he sighed, sitting down on one of the boxes facing the table and rubbed his neck. "First I get told off by Rodney, then the fact that it's my birthday, this blasted storm, and now I get locked in a room in an unexplored part of the city. Can this get any worse?"

He leaned back against the box behind him and stared at the table. Suddenly, his eyes widened.

"Oh, crap."

* * *

"_Rodney?"_

"What?!"

"_Someone woke up on the wrong side of the bed this morning," Elizabeth quipped._

"Sorry," Rodney leaned against a wall just outside the Jumper Bay. "I've been trying to track John down. If he's somewhere in the immediate vicinity, laughing at me, I'll kill him. Or better yet, I'll take him out to that Wraith cruiser, then kill him. Or, no, I'll drag him to the party, take him out to the cruiser, then I'll kill him."

"_As much as I find this amusing, Rodney," _Elizabeth cut in, _"we are running out of time. Maybe we should consider calling him."_

"Yeah, alright. Just give me a few minutes. I still have to check -"

"_Now, Rodney. Call me when you find him. Elizabeth out."_

Rodney shook his head. "Alright, John. Where are you hiding? I bet you doubled back to your quarters. That's it!" Rodney hurried down to his friend's quarters, only to find it as empty as he left it. He fought against his rising panic. "Stay calm, Rodney," he said, "there is nothing to get upset about. I'm sure he is fine and just in case, I'll go up to the Control Tower to look for his life signs."

He repeated that mantra and would've believed it, too... if the lights hadn't gone out completely.

* * *

Sorry about the delay. I am under pressure here, and I think I've gotten over my block. 


End file.
